I'm another GNU/Linux user, using Emacs org-mode as my main organizer. I had previously been using something called 'howm' for Emacs, which was good but quirky and unmaintained (afaict). Org seems to be good for the one-big-text-file approach. Planner looks good, too, but it seems like it takes a bit of buy-in before you can really get going with it. The good thing about org-mode is that it is part of Emacs now (in cvs), and works with the emacs diary. The one thing I really don't like about it is weak support for in-file links.

I still use Evolution for mail (despite using Gnus for news and being able, potentially, to use it for mail), and have come up with a way of keeping an empty inbox while keeping 'live' mails visible. I mark mails that have an associated next action as 'Important', and file them wherever they would end up filed when I'm done with them. Then I have a vfolder that shows all mails flagged 'Important'. When the task associated with a mail is done, I unflag it, and it's already filed. This way, nothing stays in my IMAP inbox.